The first commit for boosting

.gitignore

+*~
+*.swp
+*.pyc
+bin
+eggs
+parts
+.installed.cfg
+.mr.developer.cfg
+*.egg-info
+src
+develop-eggs
+sphinx
+dist

MANIFEST.in

+include README.rst bootstrap.py buildout.cfg
+recursive-include docs *.py *.rst

bootstrap.py

+##############################################################################
+#
+# Copyright (c) 2006 Zope Foundation and Contributors.
+# All Rights Reserved.
+#
+# This software is subject to the provisions of the Zope Public License,
+# Version 2.1 (ZPL).  A copy of the ZPL should accompany this distribution.
+# THIS SOFTWARE IS PROVIDED "AS IS" AND ANY AND ALL EXPRESS OR IMPLIED
+# WARRANTIES ARE DISCLAIMED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF TITLE, MERCHANTABILITY, AGAINST INFRINGEMENT, AND FITNESS
+# FOR A PARTICULAR PURPOSE.
+#
+##############################################################################
+"""Bootstrap a buildout-based project
+
+Simply run this script in a directory containing a buildout.cfg.
+The script accepts buildout command-line options, so you can
+use the -c option to specify an alternate configuration file.
+"""
+
+import os
+import shutil
+import sys
+import tempfile
+
+from optparse import OptionParser
+
+tmpeggs = tempfile.mkdtemp()
+
+usage = '''\
+[DESIRED PYTHON FOR BUILDOUT] bootstrap.py [options]
+
+Bootstraps a buildout-based project.
+
+Simply run this script in a directory containing a buildout.cfg, using the
+Python that you want bin/buildout to use.
+
+Note that by using --find-links to point to local resources, you can keep
+this script from going over the network.
+'''
+
+parser = OptionParser(usage=usage)
+parser.add_option("-v", "--version", help="use a specific zc.buildout version")
+
+parser.add_option("-t", "--accept-buildout-test-releases",
+                  dest='accept_buildout_test_releases',
+                  action="store_true", default=False,
+                  help=("Normally, if you do not specify a --version, the "
+                        "bootstrap script and buildout gets the newest "
+                        "*final* versions of zc.buildout and its recipes and "
+                        "extensions for you.  If you use this flag, "
+                        "bootstrap and buildout will get the newest releases "
+                        "even if they are alphas or betas."))
+parser.add_option("-c", "--config-file",
+                  help=("Specify the path to the buildout configuration "
+                        "file to be used."))
+parser.add_option("-f", "--find-links",
+                  help=("Specify a URL to search for buildout releases"))
+
+
+options, args = parser.parse_args()
+
+######################################################################
+# load/install setuptools
+
+to_reload = False
+try:
+    import pkg_resources
+    import setuptools
+except ImportError:
+    ez = {}
+
+    try:
+        from urllib.request import urlopen
+    except ImportError:
+        from urllib2 import urlopen
+
+    # XXX use a more permanent ez_setup.py URL when available.
+    exec(urlopen('https://bitbucket.org/pypa/setuptools/raw/0.7.2/ez_setup.py'
+                ).read(), ez)
+    setup_args = dict(to_dir=tmpeggs, download_delay=0)
+    ez['use_setuptools'](**setup_args)
+
+    if to_reload:
+        reload(pkg_resources)
+    import pkg_resources
+    # This does not (always?) update the default working set.  We will
+    # do it.
+    for path in sys.path:
+        if path not in pkg_resources.working_set.entries:
+            pkg_resources.working_set.add_entry(path)
+
+######################################################################
+# Try to best guess the version of buildout given setuptools
+if options.version is None:
+
+  try:
+    from distutils.version import LooseVersion
+    package = pkg_resources.require('setuptools')[0]
+    v = LooseVersion(package.version)
+    if v < LooseVersion('0.7'):
+      options.version = '2.1.1'
+  except:
+    pass
+
+######################################################################
+# Install buildout
+
+ws = pkg_resources.working_set
+
+cmd = [sys.executable, '-c',
+       'from setuptools.command.easy_install import main; main()',
+       '-mZqNxd', tmpeggs]
+
+find_links = os.environ.get(
+    'bootstrap-testing-find-links',
+    options.find_links or
+    ('http://downloads.buildout.org/'
+     if options.accept_buildout_test_releases else None)
+    )
+if find_links:
+    cmd.extend(['-f', find_links])
+
+setuptools_path = ws.find(
+    pkg_resources.Requirement.parse('setuptools')).location
+
+requirement = 'zc.buildout'
+version = options.version
+if version is None and not options.accept_buildout_test_releases:
+    # Figure out the most recent final version of zc.buildout.
+    import setuptools.package_index
+    _final_parts = '*final-', '*final'
+
+    def _final_version(parsed_version):
+        for part in parsed_version:
+            if (part[:1] == '*') and (part not in _final_parts):
+                return False
+        return True
+    index = setuptools.package_index.PackageIndex(
+        search_path=[setuptools_path])
+    if find_links:
+        index.add_find_links((find_links,))
+    req = pkg_resources.Requirement.parse(requirement)
+    if index.obtain(req) is not None:
+        best = []
+        bestv = None
+        for dist in index[req.project_name]:
+            distv = dist.parsed_version
+            if _final_version(distv):
+                if bestv is None or distv > bestv:
+                    best = [dist]
+                    bestv = distv
+                elif distv == bestv:
+                    best.append(dist)
+        if best:
+            best.sort()
+            version = best[-1].version
+if version:
+    requirement = '=='.join((requirement, version))
+cmd.append(requirement)
+
+import subprocess
+if subprocess.call(cmd, env=dict(os.environ, PYTHONPATH=setuptools_path)) != 0:
+    raise Exception(
+        "Failed to execute command:\n%s",
+        repr(cmd)[1:-1])
+
+######################################################################
+# Import and run buildout
+
+ws.add_entry(tmpeggs)
+ws.require(requirement)
+import zc.buildout.buildout
+
+if not [a for a in args if '=' not in a]:
+    args.append('bootstrap')
+
+# if -c was provided, we push it back into args for buildout' main function
+if options.config_file is not None:
+    args[0:0] = ['-c', options.config_file]
+
+zc.buildout.buildout.main(args)
+shutil.rmtree(tmpeggs)
+

buildout.cfg

+; vim: set fileencoding=utf-8 :
+; Andre Anjos <andre.anjos@idiap.ch>
+; Mon 16 Apr 08:29:18 2012 CEST
+
+[buildout]
+parts = scripts
+develop = .
+eggs = xbob.boosting
+newest = false
+
+[scripts]
+recipe = xbob.buildout:scripts
+dependent-scripts = true

docs/conf.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Andre Anjos <andre.anjos@idiap.ch>
+# Mon 13 Aug 2012 12:38:15 CEST
+#
+# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, version 3 of the License.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = [
+  'sphinx.ext.todo',
+  'sphinx.ext.coverage',
+  'sphinx.ext.pngmath',
+  'sphinx.ext.ifconfig',
+  'sphinx.ext.autodoc',
+  'sphinx.ext.autosummary',
+  'sphinx.ext.doctest',
+  'sphinx.ext.intersphinx',
+  #'bob.sphinxext.plot', # ours add source copying to install directory
+  ]
+
+# The viewcode extension appeared only on Sphinx >= 1.0.0
+import sphinx
+if sphinx.__version__ >= "1.0":
+  extensions.append('sphinx.ext.viewcode')
+
+# Always includes todos
+todo_include_todos = True
+
+# If we are on OSX, the 'dvipng' path maybe different
+dvipng_osx = '/opt/local/libexec/texlive/binaries/dvipng'
+if os.path.exists(dvipng_osx): pngmath_dvipng = dvipng_osx
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'Bob Project Example'
+import time
+copyright = u'%s, Idiap Research Institute' % time.strftime('%Y')
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '1.0'
+# The full version, including alpha/beta/rc tags.
+release = '1.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+#exclude_patterns = ['**/links.rst']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+if sphinx.__version__ >= "1.0":
+  html_theme = 'nature'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = 'bob'
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = ''
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+html_favicon = ''
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'bobdbdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+latex_paper_size = 'a4'
+
+# The font size ('10pt', '11pt' or '12pt').
+latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'example_man.tex', u'Bob',
+   u'Biometrics Group, Idiap Research Institute', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = ''
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+# Included after all input documents
+rst_epilog = ''
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'bob.project.example', u'Bob Project Example Documentation', [u'Idiap Research Institute'], 1)
+]
+
+
+# We want to remove all private (i.e. _. or __.__) members 
+# that are not in the list of accepted functions
+accepted_private_functions = ['__call__']
+
+def member_function_test(app, what, name, obj, skip, options):
+  # test if we have a private function
+  if len(name) > 1 and name[0] == '_':
+    # test if this private function should be allowed
+    if name not in accepted_private_functions:
+      # omit privat functions that are not in the list of accepted private functions
+      return True
+    else:
+      # test if the method is documented
+      if not hasattr(obj, '__doc__') or not obj.__doc__:
+        return True
+  
+  # Skips selected members in auto-generated documentation. Unfortunately, old
+  # versions of Boost.Python will not generate a __self__ member for static
+  # methods and that screws-up Sphinx processing. 
+  if sphinx.__version__ < "1.0":
+    # We have to remove objects that do not have a __self__ attribute set
+    import types
+    if isinstance(obj, types.BuiltinFunctionType) and \
+      not hasattr(obj, '__self__') and what == 'class':
+        app.warn("Skipping %s %s (no __self__)" % (what, name))
+        return True
+
+    return False
+  
+# Default processing flags for sphinx
+autoclass_content = 'both'
+autodoc_member_order = 'bysource'
+autodoc_default_flags = ['members', 'undoc-members', 'special-members', 'inherited-members', 'show-inheritance']
+
+def setup(app):
+  app.connect('autodoc-skip-member', member_function_test)

docs/index.rst

+.. vim: set fileencoding=utf-8 :
+.. Andre Anjos <andre.anjos@idiap.ch>
+.. Mon 13 Aug 2012 12:36:40 CEST 
+
+=====================
+ Bob Project Example
+=====================
+
+Script Documentation
+--------------------
+
+.. automodule:: example.script.version

setup.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Andre Anjos <andre.anjos@idiap.ch>
+# Mon 16 Apr 08:18:08 2012 CEST
+
+# This file contains the python (distutils/setuptools) instructions so your
+# package can be installed on **any** host system. It defines some basic
+# information like the package name for instance, or its homepage.
+#
+# It also defines which other packages this python package depends on and that
+# are required for this package's operation. The python subsystem will make
+# sure all dependent packages are installed or will install them for you upon
+# the installation of this package.
+#
+# The 'buildout' system we use here will go further and wrap this package in
+# such a way to create an isolated python working environment. Buildout will
+# make sure that dependencies which are not yet installed do get installed, but
+# **without** requiring adminstrative privileges on the host system. This
+# allows you to test your package with new python dependencies w/o requiring
+# administrative interventions.
+
+from setuptools import setup, find_packages
+
+# The only thing we do in this file is to call the setup() function with all
+# parameters that define our package.
+setup(
+
+    # This is the basic information about your project. Modify all this
+    # information before releasing code publicly.
+    name='xbob.boosting',
+    version='0.1',
+    description='Boosting framework for the BOB',
+
+    url='http://github.com/bioidiap/xbob.boosting',
+    license='GPLv3',
+    author='Rakesh mehta',
+    author_email='rakesh.mehta@idiap.ch',
+
+    # If you have a better, long description of your package, place it on the
+    # 'doc' directory and then hook it here
+    long_description=open('README.rst').read(),
+
+    # This line is required for any distutils based packaging.
+    packages=find_packages(),
+    include_package_data=True,
+
+    # This line defines which packages should be installed when you "install"
+    # this package. All packages that are mentioned here, but are not installed
+    # on the current system will be installed locally and only visible to the
+    # scripts of this package. Don't worry - You won't need adminstrative
+    # privileges when using buildout.
+    install_requires=[
+      'setuptools',
+      'bob', # base signal proc./machine learning library
+      'xbob.db.mnist',
+    ],
+
+    # Your project should be called something like 'xbob.<foo>' or 
+    # 'xbob.<foo>.<bar>'. To implement this correctly and still get all your
+    # packages to be imported w/o problems, you need to implement namespaces
+    # on the various levels of the package and declare them here. See more
+    # about this here:
+    # http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
+    #
+    # Our database packages are good examples of namespace implementations
+    # using several layers. You can check them out here:
+    # https://github.com/idiap/bob/wiki/Satellite-Packages
+    namespace_packages = [
+      'xbob',
+    ],
+
+    # This entry defines which scripts you will have inside the 'bin' directory
+    # once you install the package (or run 'bin/buildout'). The order of each
+    # entry under 'console_scripts' is like this:
+    #   script-name-at-bin-directory = module.at.your.library:function
+    #
+    # The module.at.your.library is the python file within your library, using
+    # the python syntax for directories (i.e., a '.' instead of '/' or '\').
+    # This syntax also omits the '.py' extension of the filename. So, a file
+    # installed under 'example/foo.py' that contains a function which
+    # implements the 'main()' function of particular script you want to have
+    # should be referred as 'example.foo:main'.
+    #
+    # In this simple example we will create a single program that will print
+    # the version of bob.
+    entry_points={
+
+      # scripts should be declared using this entry:
+      'console_scripts': [
+        'mnist_binary_all.py = xbob.boosting.scripts.mnist_binary_all:main',
+        'mnist_binary_one.py = xbob.boosting.scripts.mnist_binary_one:main',
+        ],
+
+      # tests that are _exported_ (that can be executed by other packages) can
+      # be signalized like this:
+      #'bob.test': [
+      #   'example = xbob.example.test:MyTests',
+      #   ],
+
+      # finally, if you are writing a database package, you must declare the
+      # relevant entries like this:
+      #'bob.db': [
+      #  'example = xbob.example.driver:Interface',
+      #  ]
+      # Note: this is just an example, this package does not declare databases
+      },
+
+    # Classifiers are important if you plan to distribute this package through
+    # PyPI. You can find the complete list of classifiers that are valid and
+    # useful here (http://pypi.python.org/pypi?%3Aaction=list_classifiers).
+    classifiers = [
+      'Development Status :: 4 - Beta',
+      'Intended Audience :: Developers',
+      'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+      'Natural Language :: English',
+      'Programming Language :: Python',
+      'Topic :: Scientific/Engineering :: Artificial Intelligence',
+      ],
+)

xbob/__init__.py

+#see http://peak.telecommunity.com/DevCenter/setuptools#namespace-packages
+__import__('pkg_resources').declare_namespace(__name__)

xbob/boosting/__init__.py

+